What a desperately cruel night for Kei Nishikori. There was hardly a soul in the house who did not feel for him when his failing body gave up on him after he had moved to within a few well-placed strokes of winning the Madrid Open and handing Rafael Nadal his third clay-court defeat of the season. Nishikori's chances of making it to the French Open, which starts in a fortnight, must be in the balance. Almost certainly he will withdraw from this week's Rome Masters.

Having just become the first Japanese player to break into the world top 10 – moving to within about 600 points of Andy Murray – Nishikori had only to serve out the second set to secure his 16th win in a row and his first title here when, turning violently to retrieve on the baseline, he broke into a limp.

He was pretty much in control of the match at 6-2, 4-3 and 15-30 after a frenzied hour and a quarter when a late flick of Nadal's iron-strong wrist put the ball beyond his reach on the backhand side.

Nishikori's eyes filled with pain as he went to the ground for treatment – as he had done when battling through the same injury to beat the Spaniard David Ferrer in an extraordinary semi-final the previous evening. He lost the second set 6-4 and struggled on to 3-0 down in the third before walking disconsolately to his chair.

Nishikori, who said he had felt a twinge in Nadal's service game at 4-2, told the crowd: "I'm very sorry for what's happened. This is my first final and I was very excited. Unfortunately I was hurting already and trying to fight, but Rafa was too good. It was my hip, actually everywhere. My leg was hurting too."

Nadal, almost sheepishly, turned to the loser and said: "Kei, I hope you recover and I wish you all the best for the rest of the season."

It is 10 years since Nadal lost three matches on clay in a single season. Had he not been gifted the win here, he surely would have had to wonder about his chances of winning a ninth French Open title. He has Rome in which to repair his confidence.

Nishikori caught him colder than a polar bear, playing without fear, and raced to 5-1 in the first set before the post-dinner stragglers had taken their seats. Nadal was powerless to stop him serving out.

In the second set, Nishikori was out-hitting the strongest forehand bully in the game for raw power – 128kph (79.5mph) average to 119kph – and that made the difference on the killer points. He needed only to hold his nerve (easily enough said) and a great scalp was his, along with a cheque for $698,720 (£414,842) and a 1,000 ranking points.